Starting phenix.real_space_refine
on Tue Jan 14 11:55:31 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9j4x_61138/01_2025/9j4x_61138.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j4x_61138/01_2025/9j4x_61138.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j4x_61138/01_2025/9j4x_61138.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j4x_61138/01_2025/9j4x_61138.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j4x_61138/01_2025/9j4x_61138.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j4x_61138/01_2025/9j4x_61138.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.103
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      30      5.16       5
     C    4462      2.51       5
     N    1024      2.21       5
     O    1068      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6588
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3186
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 14, 'TRANS': 367}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3186
          Classifications: {'peptide': 382}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 367}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 108
          Unusual residues: {'PC1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 108
          Unusual residues: {'PC1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.52, per 1000 atoms: 0.69
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (125.19, 66.34, 75.97, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       4     15.00
     O    1068      8.00
     N    1024      7.00
     C    4462      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.68
  Conformation dependent library (CDL) restraints added in 941.1 milliseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 0 sheets defined
      79.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 258
    Processing helix  chain 'A' and resid 267 through 296
      removed outlier: 3.686A  pdb=" N   ILE A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   ARG A 273 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 312 through 336
    Processing helix  chain 'A' and resid 337 through 340
      removed outlier: 3.530A  pdb=" N   SER A 340 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 337 through 340'
    Processing helix  chain 'A' and resid 345 through 360
      removed outlier: 3.979A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 390 through 403
      removed outlier: 3.571A  pdb=" N   ASN A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 420
      removed outlier: 3.723A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 453
      removed outlier: 3.575A  pdb=" N   CYS A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 471
    Processing helix  chain 'A' and resid 472 through 503
      removed outlier: 3.934A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ASN A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ALA A 480 " --> pdb=" O   HIS A 476 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG A 502 " --> pdb=" O   THR A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 4.334A  pdb=" N   LEU A 513 " --> pdb=" O   VAL A 509 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TRP A 528 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 582
      removed outlier: 4.081A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 618
      Proline residue:  A 598  - end of helix
      removed outlier: 3.750A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 623
      removed outlier: 3.605A  pdb=" N   GLU A 622 " --> pdb=" O   ASN A 619 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   PHE A 623 " --> pdb=" O   CYS A 620 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 619 through 623'
    Processing helix  chain 'B' and resid 230 through 257
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 4.782A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 312 through 336
    Processing helix  chain 'B' and resid 345 through 360
      removed outlier: 4.081A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'B' and resid 384 through 387
    Processing helix  chain 'B' and resid 390 through 417
      removed outlier: 5.940A  pdb=" N   VAL B 405 " --> pdb=" O   ASN B 401 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 453
    Processing helix  chain 'B' and resid 453 through 471
    Processing helix  chain 'B' and resid 472 through 499
      removed outlier: 4.285A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   VAL B 478 " --> pdb=" O   PHE B 474 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.588A  pdb=" N   PHE B 510 " --> pdb=" O   ASP B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 581
      removed outlier: 3.522A  pdb=" N   TYR B 560 " --> pdb=" O   LYS B 556 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER B 581 " --> pdb=" O   ILE B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 619
      Proline residue:  B 598  - end of helix
      removed outlier: 3.760A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 620 through 623
      removed outlier: 4.414A  pdb=" N   PHE B 623 " --> pdb=" O   CYS B 620 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 620 through 623'

    438 hydrogen bonds defined for protein.
    1311 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.61

  Time building geometry restraints manager: 1.91 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 989
        1.32 -     1.44: 2066
        1.44 -     1.57: 3691
        1.57 -     1.69: 8
        1.69 -     1.81: 42
  Bond restraints: 6796
  Sorted by residual:
  bond pdb=" CG  GLN A 399 "
       pdb=" CD  GLN A 399 "
    ideal  model  delta    sigma   weight residual
    1.516  1.492  0.024 2.50e-02 1.60e+03 9.11e-01
  bond pdb=" C   ALA A 337 "
       pdb=" N   PRO A 338 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 8.26e-01
  bond pdb=" N   GLY A 589 "
       pdb=" CA  GLY A 589 "
    ideal  model  delta    sigma   weight residual
    1.449  1.461 -0.012 1.45e-02 4.76e+03 6.89e-01
  bond pdb=" C   VAL B 567 "
       pdb=" O   VAL B 567 "
    ideal  model  delta    sigma   weight residual
    1.237  1.246 -0.009 1.13e-02 7.83e+03 6.38e-01
  bond pdb=" CB  CYS B 463 "
       pdb=" SG  CYS B 463 "
    ideal  model  delta    sigma   weight residual
    1.808  1.783  0.025 3.30e-02 9.18e+02 5.56e-01
  ... (remaining 6791 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 8820
        1.11 -     2.21: 315
        2.21 -     3.32: 39
        3.32 -     4.43: 14
        4.43 -     5.53: 14
  Bond angle restraints: 9202
  Sorted by residual:
  angle pdb=" N   GLU A 260 "
        pdb=" CA  GLU A 260 "
        pdb=" C   GLU A 260 "
      ideal   model   delta    sigma   weight residual
     114.62  109.21    5.41 1.14e+00 7.69e-01 2.26e+01
  angle pdb=" CA  GLU A 260 "
        pdb=" C   GLU A 260 "
        pdb=" N   THR A 261 "
      ideal   model   delta    sigma   weight residual
     119.71  115.09    4.62 1.17e+00 7.31e-01 1.56e+01
  angle pdb=" N   ARG A 270 "
        pdb=" CA  ARG A 270 "
        pdb=" C   ARG A 270 "
      ideal   model   delta    sigma   weight residual
     114.75  110.75    4.00 1.26e+00 6.30e-01 1.01e+01
  angle pdb=" C   ILE A 269 "
        pdb=" N   ARG A 270 "
        pdb=" CA  ARG A 270 "
      ideal   model   delta    sigma   weight residual
     121.52  126.81   -5.29 1.74e+00 3.30e-01 9.23e+00
  angle pdb=" N   VAL A 509 "
        pdb=" CA  VAL A 509 "
        pdb=" C   VAL A 509 "
      ideal   model   delta    sigma   weight residual
     113.00  109.06    3.94 1.30e+00 5.92e-01 9.17e+00
  ... (remaining 9197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.54: 3592
       16.54 -    33.08: 236
       33.08 -    49.61: 62
       49.61 -    66.15: 25
       66.15 -    82.69: 3
  Dihedral angle restraints: 3918
    sinusoidal: 1668
      harmonic: 2250
  Sorted by residual:
  dihedral pdb=" CA  ILE A 269 "
           pdb=" C   ILE A 269 "
           pdb=" N   ARG A 270 "
           pdb=" CA  ARG A 270 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.18   31.82     0      5.00e+00 4.00e-02 4.05e+01
  dihedral pdb=" CA  PHE A 257 "
           pdb=" C   PHE A 257 "
           pdb=" N   LYS A 258 "
           pdb=" CA  LYS A 258 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.24  -18.76     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  THR A 383 "
           pdb=" C   THR A 383 "
           pdb=" N   ALA A 384 "
           pdb=" CA  ALA A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.29  -17.71     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 3915 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 659
       0.035 -    0.069: 239
       0.069 -    0.103: 73
       0.103 -    0.138: 13
       0.138 -    0.172: 2
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" CB  ILE A 269 "
            pdb=" CA  ILE A 269 "
            pdb=" CG1 ILE A 269 "
            pdb=" CG2 ILE A 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.42e-01
  chirality pdb=" CA  TRP A 266 "
            pdb=" N   TRP A 266 "
            pdb=" C   TRP A 266 "
            pdb=" CB  TRP A 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.42e-01
  chirality pdb=" CA  ILE A 342 "
            pdb=" N   ILE A 342 "
            pdb=" C   ILE A 342 "
            pdb=" CB  ILE A 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 983 not shown)

  Planarity restraints: 1098
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 563 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   ILE A 563 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ILE A 563 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE A 564 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 566 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.81e+00
        pdb=" C   ASP A 566 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ASP A 566 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL A 567 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 306 "    0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO A 307 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 307 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 307 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1095 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 101
        2.69 -     3.24: 6660
        3.24 -     3.80: 11036
        3.80 -     4.35: 14289
        4.35 -     4.90: 24201
  Nonbonded interactions: 56287
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 271 "
            pdb=" OH  TYR A 352 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" O   LYS B 482 "
            pdb=" OG1 THR B 485 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OE1 GLU B 318 "
            pdb=" OH  TYR B 367 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" NH2 ARG A 466 "
            pdb=" O   GLY A 621 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   ILE B 271 "
            pdb=" OH  TYR B 352 "
     model   vdw
     2.247 3.040
  ... (remaining 56282 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.260
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6796  Z= 0.205
  Angle     :  0.517   5.533   9202  Z= 0.294
  Chirality :  0.039   0.172    986
  Planarity :  0.004   0.033   1098
  Dihedral  : 12.984  82.689   2466
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  6.05 %
    Favored  : 92.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.30), residues: 756
  helix:  1.42 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -2.42 (0.42), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 395 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.015   0.001   PHE B 610 
 TYR   0.012   0.001   TYR A 553 
 ARG   0.002   0.000   ARG B 611 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A  318 GLU cc_start: 0.8815 (tt0) cc_final: 0.8511 (tt0)
REVERT: A  376 LYS cc_start: 0.7836 (mttt) cc_final: 0.7308 (mmtm)
REVERT: A  394 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8093 (t80)
REVERT: A  471 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7800 (mmtm)
REVERT: A  506 ASP cc_start: 0.7111 (m-30) cc_final: 0.6883 (p0)
REVERT: A  523 CYS cc_start: 0.8530 (t) cc_final: 0.8153 (m)
REVERT: A  538 ASP cc_start: 0.8084 (t70) cc_final: 0.7499 (t0)
REVERT: B  265 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7777 (pp)
REVERT: B  472 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7326 (mtm110)
REVERT: B  497 SER cc_start: 0.8204 (m) cc_final: 0.7959 (p)
REVERT: B  508 MET cc_start: 0.7624 (mmm) cc_final: 0.6439 (mtp)
REVERT: B  538 ASP cc_start: 0.7456 (t0) cc_final: 0.6865 (t0)
REVERT: B  549 GLU cc_start: 0.8354 (tt0) cc_final: 0.8140 (tt0)
REVERT: B  550 GLU cc_start: 0.7290 (pt0) cc_final: 0.6684 (pm20)
REVERT: B  608 ASN cc_start: 0.8743 (m-40) cc_final: 0.8476 (m110)
  outliers start: 9
  outliers final: 1
  residues processed: 126
  average time/residue: 1.0376
  time to fit residues: 138.6652
Evaluate side-chains
  107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  394 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.161094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.123490 restraints weight = 7076.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.58
r_work: 0.3125 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6796  Z= 0.225
  Angle     :  0.535   7.758   9202  Z= 0.289
  Chirality :  0.041   0.179    986
  Planarity :  0.004   0.041   1098
  Dihedral  : 12.437  64.547   1038
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.62 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.30), residues: 756
  helix:  1.95 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.38 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 395 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.022   0.002   PHE B 511 
 TYR   0.018   0.002   TYR A 352 
 ARG   0.003   0.000   ARG B 448 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  376 LYS cc_start: 0.7897 (mttt) cc_final: 0.7421 (mmtm)
REVERT: A  471 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7908 (mmtm)
REVERT: A  523 CYS cc_start: 0.8857 (t) cc_final: 0.8540 (m)
REVERT: A  538 ASP cc_start: 0.8234 (t70) cc_final: 0.7638 (t0)
REVERT: A  622 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7959 (mt-10)
REVERT: B  265 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7730 (pp)
REVERT: B  301 LEU cc_start: 0.9296 (tp) cc_final: 0.9095 (tp)
REVERT: B  497 SER cc_start: 0.8338 (m) cc_final: 0.8027 (p)
REVERT: B  508 MET cc_start: 0.7726 (mmm) cc_final: 0.6557 (mtp)
REVERT: B  538 ASP cc_start: 0.7729 (t0) cc_final: 0.7183 (t0)
REVERT: B  549 GLU cc_start: 0.8463 (tt0) cc_final: 0.8231 (tt0)
REVERT: B  550 GLU cc_start: 0.7092 (pt0) cc_final: 0.6625 (pm20)
REVERT: B  577 ILE cc_start: 0.7422 (tt) cc_final: 0.7059 (pt)
REVERT: B  608 ASN cc_start: 0.8726 (m-40) cc_final: 0.8489 (m110)
  outliers start: 15
  outliers final: 5
  residues processed: 118
  average time/residue: 0.9501
  time to fit residues: 119.9057
Evaluate side-chains
  106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  447 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0980
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN
A 576 GLN
B 310 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.159512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.121980 restraints weight = 7201.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.58
r_work: 0.3089 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6796  Z= 0.268
  Angle     :  0.550   6.994   9202  Z= 0.293
  Chirality :  0.042   0.182    986
  Planarity :  0.004   0.036   1098
  Dihedral  : 12.517  64.355   1036
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.54 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.30), residues: 756
  helix:  1.88 (0.21), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.31 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 395 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.016   0.002   PHE A 605 
 TYR   0.024   0.002   TYR A 496 
 ARG   0.003   0.000   ARG B 270 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.632 
Fit side-chains
REVERT: A  376 LYS cc_start: 0.7921 (mttt) cc_final: 0.7433 (mmtm)
REVERT: A  523 CYS cc_start: 0.8941 (t) cc_final: 0.8590 (m)
REVERT: A  538 ASP cc_start: 0.8270 (t70) cc_final: 0.7673 (t0)
REVERT: A  622 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7889 (mt-10)
REVERT: B  265 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7697 (pp)
REVERT: B  270 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7814 (mtm110)
REVERT: B  497 SER cc_start: 0.8383 (m) cc_final: 0.8020 (p)
REVERT: B  508 MET cc_start: 0.7755 (mmm) cc_final: 0.6559 (mtp)
REVERT: B  538 ASP cc_start: 0.7746 (t0) cc_final: 0.7204 (t0)
REVERT: B  549 GLU cc_start: 0.8452 (tt0) cc_final: 0.8182 (tt0)
REVERT: B  550 GLU cc_start: 0.7115 (pt0) cc_final: 0.6706 (pm20)
REVERT: B  577 ILE cc_start: 0.7605 (tt) cc_final: 0.7132 (pt)
  outliers start: 19
  outliers final: 8
  residues processed: 115
  average time/residue: 0.9652
  time to fit residues: 118.6815
Evaluate side-chains
  108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN
A 576 GLN
B 310 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.159158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.121804 restraints weight = 7267.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.57
r_work: 0.3104 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6796  Z= 0.229
  Angle     :  0.530   6.833   9202  Z= 0.284
  Chirality :  0.041   0.182    986
  Planarity :  0.004   0.038   1098
  Dihedral  : 12.359  64.607   1034
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.57 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.30), residues: 756
  helix:  1.97 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.31 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 395 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.016   0.002   PHE B 610 
 TYR   0.024   0.002   TYR A 496 
 ARG   0.004   0.000   ARG A 448 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A  259 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6621 (tt)
REVERT: A  376 LYS cc_start: 0.7895 (mttt) cc_final: 0.7419 (mmtm)
REVERT: A  394 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7847 (t80)
REVERT: A  471 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7925 (mmtt)
REVERT: A  523 CYS cc_start: 0.8972 (t) cc_final: 0.8610 (m)
REVERT: B  265 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7672 (pp)
REVERT: B  472 ARG cc_start: 0.7662 (mtm110) cc_final: 0.7097 (mtp85)
REVERT: B  497 SER cc_start: 0.8401 (m) cc_final: 0.7948 (p)
REVERT: B  508 MET cc_start: 0.7718 (mmm) cc_final: 0.6536 (mtp)
REVERT: B  538 ASP cc_start: 0.7739 (t0) cc_final: 0.7191 (t0)
REVERT: B  577 ILE cc_start: 0.7659 (tt) cc_final: 0.7184 (pt)
  outliers start: 18
  outliers final: 7
  residues processed: 117
  average time/residue: 0.9348
  time to fit residues: 117.0998
Evaluate side-chains
  108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  550 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0970
   chunk 7 optimal weight:    0.4980
   chunk 53 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0980
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.4178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.161591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.125435 restraints weight = 7217.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.50
r_work: 0.3178 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6796  Z= 0.172
  Angle     :  0.497   6.669   9202  Z= 0.268
  Chirality :  0.039   0.174    986
  Planarity :  0.004   0.038   1098
  Dihedral  : 12.114  63.285   1034
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.75 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.30), residues: 756
  helix:  2.10 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.13 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 395 
 HIS   0.003   0.001   HIS B 313 
 PHE   0.016   0.001   PHE B 610 
 TYR   0.026   0.002   TYR A 496 
 ARG   0.004   0.000   ARG A 448 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A  376 LYS cc_start: 0.7767 (mttt) cc_final: 0.7278 (mmtm)
REVERT: A  470 THR cc_start: 0.8543 (m) cc_final: 0.8151 (p)
REVERT: A  471 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7934 (mmtt)
REVERT: A  472 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7710 (mtp180)
REVERT: A  523 CYS cc_start: 0.8830 (t) cc_final: 0.8475 (m)
REVERT: A  538 ASP cc_start: 0.8219 (t70) cc_final: 0.7525 (t0)
REVERT: A  622 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7791 (mt-10)
REVERT: B  265 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7658 (pp)
REVERT: B  394 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7736 (t80)
REVERT: B  472 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7081 (mtp85)
REVERT: B  497 SER cc_start: 0.8365 (m) cc_final: 0.7817 (p)
REVERT: B  508 MET cc_start: 0.7604 (mmm) cc_final: 0.6424 (mtp)
REVERT: B  538 ASP cc_start: 0.7681 (t0) cc_final: 0.7142 (t0)
REVERT: B  550 GLU cc_start: 0.7096 (pt0) cc_final: 0.6657 (pm20)
REVERT: B  577 ILE cc_start: 0.7547 (tt) cc_final: 0.7076 (pt)
REVERT: B  608 ASN cc_start: 0.8651 (m-40) cc_final: 0.8367 (m110)
  outliers start: 15
  outliers final: 7
  residues processed: 117
  average time/residue: 0.9490
  time to fit residues: 118.6571
Evaluate side-chains
  104 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  550 GLU
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.158173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.120874 restraints weight = 7156.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.56
r_work: 0.3094 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6796  Z= 0.276
  Angle     :  0.557   7.990   9202  Z= 0.294
  Chirality :  0.042   0.228    986
  Planarity :  0.004   0.040   1098
  Dihedral  : 12.411  65.731   1034
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 13.86 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.30), residues: 756
  helix:  1.84 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -2.28 (0.42), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 573 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.016   0.002   PHE A 605 
 TYR   0.027   0.002   TYR B 496 
 ARG   0.004   0.000   ARG B 270 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 LYS cc_start: 0.7914 (mttt) cc_final: 0.7427 (mmtm)
REVERT: A  394 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7870 (t80)
REVERT: A  470 THR cc_start: 0.8492 (m) cc_final: 0.8097 (p)
REVERT: A  471 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7986 (mmtt)
REVERT: A  523 CYS cc_start: 0.8939 (t) cc_final: 0.8580 (m)
REVERT: A  538 ASP cc_start: 0.8280 (t70) cc_final: 0.7587 (t0)
REVERT: A  622 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7918 (mt-10)
REVERT: B  265 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7636 (pp)
REVERT: B  354 PHE cc_start: 0.8324 (t80) cc_final: 0.8122 (t80)
REVERT: B  394 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7796 (t80)
REVERT: B  472 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7112 (mtp85)
REVERT: B  497 SER cc_start: 0.8401 (m) cc_final: 0.7847 (p)
REVERT: B  508 MET cc_start: 0.7689 (mmm) cc_final: 0.6483 (mtp)
REVERT: B  538 ASP cc_start: 0.7728 (t0) cc_final: 0.7172 (t0)
REVERT: B  550 GLU cc_start: 0.7158 (pt0) cc_final: 0.6693 (pm20)
REVERT: B  577 ILE cc_start: 0.7667 (tt) cc_final: 0.7170 (pt)
  outliers start: 20
  outliers final: 10
  residues processed: 108
  average time/residue: 0.9351
  time to fit residues: 107.7873
Evaluate side-chains
  107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  388 LYS
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 73 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.160819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.124522 restraints weight = 7180.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.50
r_work: 0.3153 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6796  Z= 0.219
  Angle     :  0.525   7.957   9202  Z= 0.280
  Chirality :  0.041   0.219    986
  Planarity :  0.004   0.041   1098
  Dihedral  : 12.263  63.290   1034
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.75 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.30), residues: 756
  helix:  2.00 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.09 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 573 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.017   0.001   PHE B 610 
 TYR   0.029   0.002   TYR A 496 
 ARG   0.005   0.000   ARG B 270 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 LYS cc_start: 0.7824 (mttt) cc_final: 0.7335 (mmtm)
REVERT: A  394 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7714 (t80)
REVERT: A  470 THR cc_start: 0.8481 (m) cc_final: 0.8111 (p)
REVERT: A  471 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7934 (mmtt)
REVERT: A  523 CYS cc_start: 0.8878 (t) cc_final: 0.8509 (m)
REVERT: A  538 ASP cc_start: 0.8240 (t70) cc_final: 0.7537 (t0)
REVERT: A  622 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7954 (mt-10)
REVERT: B  265 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7653 (pp)
REVERT: B  394 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7801 (t80)
REVERT: B  472 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7059 (mtp85)
REVERT: B  497 SER cc_start: 0.8354 (m) cc_final: 0.7799 (p)
REVERT: B  508 MET cc_start: 0.7629 (mmm) cc_final: 0.6433 (mtp)
REVERT: B  538 ASP cc_start: 0.7676 (t0) cc_final: 0.7099 (t0)
REVERT: B  577 ILE cc_start: 0.7623 (tt) cc_final: 0.7102 (pt)
  outliers start: 14
  outliers final: 7
  residues processed: 105
  average time/residue: 1.1670
  time to fit residues: 130.6245
Evaluate side-chains
  106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  388 LYS
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0870
   chunk 16 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 69 optimal weight:    0.4980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.3958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.162007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.125995 restraints weight = 7124.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.49
r_work: 0.3215 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6796  Z= 0.166
  Angle     :  0.498   7.910   9202  Z= 0.267
  Chirality :  0.040   0.194    986
  Planarity :  0.004   0.040   1098
  Dihedral  : 11.992  61.014   1034
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.04 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.30), residues: 756
  helix:  2.02 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -2.12 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 573 
 HIS   0.003   0.001   HIS B 313 
 PHE   0.017   0.001   PHE B 610 
 TYR   0.030   0.002   TYR A 496 
 ARG   0.005   0.000   ARG B 270 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.8729 (t80) cc_final: 0.8520 (t80)
REVERT: A  376 LYS cc_start: 0.7763 (mttt) cc_final: 0.7297 (mmtm)
REVERT: A  413 MET cc_start: 0.7814 (mtp) cc_final: 0.7456 (ttt)
REVERT: A  470 THR cc_start: 0.8467 (m) cc_final: 0.8103 (p)
REVERT: A  523 CYS cc_start: 0.8805 (t) cc_final: 0.8483 (m)
REVERT: A  538 ASP cc_start: 0.8233 (t70) cc_final: 0.7554 (t0)
REVERT: A  622 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7927 (mt-10)
REVERT: B  265 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7671 (pp)
REVERT: B  394 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7773 (t80)
REVERT: B  472 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7184 (mtp85)
REVERT: B  497 SER cc_start: 0.8300 (m) cc_final: 0.7712 (p)
REVERT: B  508 MET cc_start: 0.7570 (mmm) cc_final: 0.6450 (mtp)
REVERT: B  538 ASP cc_start: 0.7693 (t0) cc_final: 0.7141 (t0)
REVERT: B  577 ILE cc_start: 0.7631 (tt) cc_final: 0.7164 (pt)
  outliers start: 15
  outliers final: 7
  residues processed: 108
  average time/residue: 0.9432
  time to fit residues: 108.7438
Evaluate side-chains
  107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  550 GLU
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0000
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0060
   overall best weight:    0.6006

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.162621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.126382 restraints weight = 7178.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.51
r_work: 0.3180 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6796  Z= 0.208
  Angle     :  0.521   7.815   9202  Z= 0.278
  Chirality :  0.040   0.170    986
  Planarity :  0.004   0.041   1098
  Dihedral  : 12.041  61.363   1034
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.19 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.30), residues: 756
  helix:  1.98 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -2.06 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 573 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.018   0.001   PHE B 283 
 TYR   0.027   0.002   TYR B 496 
 ARG   0.005   0.000   ARG B 270 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 LYS cc_start: 0.7762 (mttt) cc_final: 0.7263 (mmtm)
REVERT: A  470 THR cc_start: 0.8439 (m) cc_final: 0.8072 (p)
REVERT: A  523 CYS cc_start: 0.8855 (t) cc_final: 0.8511 (m)
REVERT: A  538 ASP cc_start: 0.8215 (t70) cc_final: 0.7510 (t0)
REVERT: A  622 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7927 (mt-10)
REVERT: B  265 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7642 (pp)
REVERT: B  394 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7752 (t80)
REVERT: B  472 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7165 (mtp85)
REVERT: B  497 SER cc_start: 0.8307 (m) cc_final: 0.7715 (p)
REVERT: B  508 MET cc_start: 0.7517 (mmm) cc_final: 0.6352 (mtp)
REVERT: B  538 ASP cc_start: 0.7675 (t0) cc_final: 0.7102 (t0)
REVERT: B  577 ILE cc_start: 0.7568 (tt) cc_final: 0.7063 (pt)
  outliers start: 12
  outliers final: 7
  residues processed: 102
  average time/residue: 1.0191
  time to fit residues: 111.1203
Evaluate side-chains
  107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  388 LYS
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  550 GLU
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.161250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.124928 restraints weight = 7252.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.58
r_work: 0.3153 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6796  Z= 0.216
  Angle     :  0.526   7.713   9202  Z= 0.281
  Chirality :  0.040   0.171    986
  Planarity :  0.004   0.041   1098
  Dihedral  : 12.044  60.306   1034
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.78 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.30), residues: 756
  helix:  1.93 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -2.02 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 573 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.019   0.002   PHE B 283 
 TYR   0.026   0.002   TYR B 496 
 ARG   0.005   0.000   ARG B 270 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A  376 LYS cc_start: 0.7800 (mttt) cc_final: 0.7306 (mmtm)
REVERT: A  413 MET cc_start: 0.7774 (mtp) cc_final: 0.7457 (ttt)
REVERT: A  470 THR cc_start: 0.8431 (m) cc_final: 0.8069 (p)
REVERT: A  489 MET cc_start: 0.8701 (ttp) cc_final: 0.8460 (ttp)
REVERT: A  523 CYS cc_start: 0.8884 (t) cc_final: 0.8510 (m)
REVERT: A  622 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7945 (mt-10)
REVERT: B  265 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7638 (pp)
REVERT: B  394 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7798 (t80)
REVERT: B  472 ARG cc_start: 0.7767 (mtm110) cc_final: 0.7190 (mtp85)
REVERT: B  497 SER cc_start: 0.8303 (m) cc_final: 0.7706 (p)
REVERT: B  508 MET cc_start: 0.7525 (mmm) cc_final: 0.6349 (mtp)
REVERT: B  538 ASP cc_start: 0.7677 (t0) cc_final: 0.7101 (t0)
REVERT: B  577 ILE cc_start: 0.7570 (tt) cc_final: 0.7061 (pt)
  outliers start: 11
  outliers final: 7
  residues processed: 106
  average time/residue: 0.9676
  time to fit residues: 109.6835
Evaluate side-chains
  106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  550 GLU
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  550 GLU
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.160589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.124424 restraints weight = 7267.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.57
r_work: 0.3145 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6796  Z= 0.226
  Angle     :  0.534   7.381   9202  Z= 0.286
  Chirality :  0.040   0.171    986
  Planarity :  0.004   0.041   1098
  Dihedral  : 12.042  59.388   1034
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.78 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.30), residues: 756
  helix:  1.89 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -2.00 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 573 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.021   0.002   PHE B 283 
 TYR   0.025   0.002   TYR B 496 
 ARG   0.005   0.000   ARG B 270 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4765.49 seconds
wall clock time: 85 minutes 29.27 seconds (5129.27 seconds total)